GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_1693 in Shewanella amazonensis SB2B

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate 6937828 Sama_1969 ABC transporter, ATP-binding protein (RefSeq)

Query= uniprot:A0A165KC86
         (260 letters)



>FitnessBrowser__SB2B:6937828
          Length = 301

 Score =  107 bits (268), Expect = 2e-28
 Identities = 72/220 (32%), Positives = 114/220 (51%), Gaps = 20/220 (9%)

Query: 15  ISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAGTFELAGKPYE 74
           ++KR+G   AL DV + ++ G    L+GPNGAGKTT  +++ G   PD G+ E+ G  + 
Sbjct: 9   LTKRYGSKTALDDVSLQVEAGAPVALVGPNGAGKTTLMSLMCGYIQPDGGSLEILG--HV 66

Query: 75  PTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGLFGAVFRTKGFKAEEAAI 134
           P +   + K           L  +     N  VG  +   + L       +GF A++A  
Sbjct: 67  PGSRQLLGKV--------CALPQDALLDPNFSVGEQLSFFASL-------QGFSAKDA-- 109

Query: 135 AKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALDEPAAGMNATEKV 194
            + A+ +L+ V +   A +K   LS+G  +R+ IA+AL   PQL+ LDEP AG++     
Sbjct: 110 RREAERVLELVELKDAARHKPTALSHGMGKRVAIAQALIGTPQLVLLDEPTAGLDPANAR 169

Query: 195 QLRELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYGK 234
            +RELI    ++  T L+  H+++ +  LCD V  LD GK
Sbjct: 170 AVRELISH-ASEQTTFLISSHNLEELERLCDTVLYLDKGK 208


Lambda     K      H
   0.319    0.137    0.384 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 185
Number of extensions: 5
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 260
Length of database: 301
Length adjustment: 26
Effective length of query: 234
Effective length of database: 275
Effective search space:    64350
Effective search space used:    64350
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory